tests/testthat/test_AllClasses.R

In Gviz: Plotting data and annotation information along genomic coordinates

## Classes in Gviz

test_that("ImageMap works", {
    mat <- matrix(1, ncol=4, dimnames=list("a",NULL))
    tags <- list(a=c(a="tag"))
    expect_s4_class(ImageMap(mat, tags=tags), "ImageMap")
    expect_identical(ImageMap(mat, tags=tags)@coords,mat)
    expect_identical(ImageMap(mat, tags=tags)@tags,tags)
    expect_error(ImageMap(matrix(1, ncol=3), tags=tags), "must be a numeric matrix with 4 column")
    expect_error(ImageMap(matrix(1, ncol=4), tags=tags), "Rownames must be set for the matrix in")
    expect_error(ImageMap(mat, tags=list(c(a="tag1"))), "must be a named list with character vector items.")
    expect_error(ImageMap(mat, tags=list(a=c(a="tag1", b="tag2"))), "following values in the")
    expect_error(ImageMap(mat, tags=list(a=c("tag1"))), "items in the 'tags' list must be named character")
})

test_that("DisplayPars works", {
    dp <- DisplayPars(a=1)

    expect_s4_class(dp, "DisplayPars")
    expect_identical(dp@pars$a, 1)
    expect_error(DisplayPars(1), "All supplied arguments must be named.")
    expect_error(DisplayPars(1, b=2), "All supplied arguments must be named.")
                                        # .updateDp
    expect_message(.updateDp(dp), "Note that the behaviour of the")
    expect_identical(.updateDp(dp, interactive=FALSE)@pars, list(a=1))
    dp@pars <- new.env()
    dp@pars[["a"]] <- 1
    expect_identical(.updateDp(dp, interactive=FALSE)@pars, list(a=1))
    expect_message(.updateDp(dp, interactive=FALSE), "The DisplayPars object has been updated")
    ## getPar
    expect_identical(getPar(dp), list(a=1))
    expect_identical(getPar(dp, "a"), 1)
    ## setPar
    expect_identical(setPar(dp, "b", 2, interactive=FALSE)@pars$b, 2)
    expect_error(setPar(dp, "b", c(1,2), interactive=FALSE), "equal length")
    ## displayPars <-
    displayPars(dp) <- list(b=2)
    expect_identical(dp@pars, list(a=1, b=2))
    ## getPar
    expect_identical(getPar(dp), list(a=1, b=2))
    expect_identical(getPar(dp, "a"), 1)
    ## displayPars
    expect_identical(displayPars(dp), list(a=1, b=2))
    expect_identical(displayPars(dp, "a"), 1)
    ## as.list
    expect_identical(as.list(dp), list(a=1, b=2))
})

test_that("IdeogramTrack works", {
    ideoTrack <- IdeogramTrack(chromosome="chrI", genome="sacCer3", bands=cyto.bands)
    expect_s4_class(ideoTrack, "GdObject")
    expect_s4_class(ideoTrack, "RangeTrack")
    expect_s4_class(ideoTrack, "IdeogramTrack")
})

test_that("GenomeAxisTrack works", {
    expect_s4_class(GenomeAxisTrack(), "GdObject")
    expect_s4_class(GenomeAxisTrack(), "GenomeAxisTrack")
})

test_that("DataTrack works", {
    expect_s4_class(DataTrack(), "GdObject")
    expect_s4_class(DataTrack(), "RangeTrack")
    expect_s4_class(DataTrack(), "NumericTrack")
    expect_s4_class(DataTrack(), "DataTrack")
})

test_that("AnnnotationTrack works", {
    expect_s4_class(AnnotationTrack(), "GdObject")
    expect_s4_class(AnnotationTrack(), "RangeTrack")
    expect_s4_class(AnnotationTrack(), "StackedTrack")
    expect_s4_class(AnnotationTrack(), "AnnotationTrack")

    expect_error(AnnotationTrack(stacking="allover"), "following values for 'stacking'")
})

test_that("GeneRegionTrack works", {
    expect_s4_class(GeneRegionTrack(), "AnnotationTrack")
    expect_s4_class(GeneRegionTrack(), "GeneRegionTrack")
})

test_that("BiomartGeneRegionTrack works", {
    ## expect_s4_class(BiomartGeneRegionTrack(), "BiomartGeneRegionTrack")

    biomartMapping <- list(gene_id="ensembl_gene_id",transcript_id="ensembl_transcript_id", exon_id="ensembl_exon_id",
                           start="exon_chrom_start", end="exon_chrom_end", rank="rank", strand="strand",
                           symbol=c("external_gene_name", "external_gene_id"), feature="gene_biotype", chromosome="chromosome_name",
                           u5s="5_utr_start", u5e="5_utr_end", u3s="3_utr_start", u3e="3_utr_end", cdsl=c("cds_length", "cds_start"),
                           phase="phase")
    expect_identical(.getBMFeatureMap(), biomartMapping)
})

test_that("SequenceTrack works", {
    expect_s4_class(SequenceTrack(), "GdObject")
    expect_s4_class(SequenceTrack(), "SequenceTrack")
    expect_s4_class(SequenceTrack(), "SequenceDNAStringSetTrack")
    expect_s4_class(RNASequenceTrack(), "SequenceRNAStringSetTrack")
})

test_that("AlignmentsTrack works", {
    expect_s4_class(AlignmentsTrack(), "GdObject")
    expect_s4_class(AlignmentsTrack(), "RangeTrack")
    expect_s4_class(AlignmentsTrack(), "StackedTrack")
    expect_s4_class(AlignmentsTrack(), "AlignmentsTrack")
    expect_s4_class(AlignmentsTrack(showIndels=TRUE), "AlignmentsTrack")

    expect_s4_class(AlignmentsTrack(bamfile), "ReferenceTrack")
    expect_s4_class(AlignmentsTrack(bamfile), "AlignmentsTrack")
})

test_that("CustomTrack works", {
    expect_s4_class(CustomTrack(), "GdObject")
    expect_s4_class(CustomTrack(), "CustomTrack")
})

test_that("HighlightTrack works", {
    expect_s4_class(HighlightTrack(), "GdObject")
    expect_s4_class(HighlightTrack(), "RangeTrack")
    expect_s4_class(HighlightTrack(), "HighlightTrack")

    expect_true(is(HighlightTrack()@range, "GRanges"))
    expect_error(HighlightTrack(c(annoTrack, geneModels)),
                 "All elements in 'trackList' must inherit from 'GdObject'")

    displayPars(highTrack) <- list(col="black")
    expect_identical(displayPars(highTrack)$col, "black")

    displayPars(highTrack, recursive=TRUE) <- list(col="red")
    expect_identical(vapply(highTrack@trackList, function(x) displayPars(x)$col,
                            FUN.VALUE=character(1)), "red")
})

test_that("OverlayTrack works", {
    expect_s4_class(OverlayTrack(), "GdObject")
    expect_s4_class(OverlayTrack(), "OverlayTrack")

    expect_true(is.list(OverlayTrack(annoTrack)@trackList))
    expect_error(OverlayTrack(c(annoTrack, geneModels)),
                 "All elements in 'trackList' must inherit from 'GdObject'")

    displayPars(overTrack) <- list(col="black")
    expect_identical(displayPars(overTrack)$col, "black")

    displayPars(overTrack, recursive=TRUE) <- list(col="red")
    expect_identical(vapply(overTrack@trackList, function(x) displayPars(x)$col,
                            FUN.VALUE=character(1)), c("red", "red"))
})

test_that("DetailsAnnotationTrack works", {
    expect_s4_class(DetailsAnnotationTrack(), "GdObject")
    expect_s4_class(DetailsAnnotationTrack(), "StackedTrack")
    expect_s4_class(DetailsAnnotationTrack(), "RangeTrack")
    expect_s4_class(DetailsAnnotationTrack(), "AnnotationTrack")

    expect_s4_class(detTrack, "AnnotationTrack")
    expect_identical(detTrack@selectFun, selFun)
    expect_identical(detTrack@fun, detFun)

})

test_that("md5 hash for BiomartTrack works", {
    data("biomTrack")
    expect_identical(.bmGuid(biomTrack), "b0cbf1bb0e4e5a1936fe68e36da5f210")
})

test_that("interaction with biomart works", {
    check_biomart()
    biomartTrack <- BiomartGeneRegionTrack(genome="hg38", chromosome="chr7",
                                           start=20e6, end=21e6, name="ENSEMBL")
    expect_s4_class(biomartTrack, "GdObject")
    expect_s4_class(biomartTrack, "StackedTrack")
    expect_s4_class(biomartTrack, "RangeTrack")
    expect_s4_class(biomartTrack, "AnnotationTrack")
    expect_s4_class(biomartTrack, "GeneRegionTrack")
    expect_s4_class(biomartTrack, "BiomartGeneRegionTrack")
})